ArticleActa crystallographica. Section D, Structural biology2023
Likelihood-based docking of models into cryo-EM maps.
Article in Acta crystallographica. Section D, Structural biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Breadth of ACE2 receptor usage predicts host range and antigenic relatedness across bat sarbecoviruses.PLoS biology · 2026Article
- Structural basis of stepwise G protein activation by the viral chemokine receptor US28.bioRxiv : the preprint server for biology · 2026Article
- AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network.Nature methods · 2026Article
- Cryo-EM Analysis in CASP16.Proteins · 2026Article
- Model Quality Assessment for CASP16.Proteins · 2026Article
- High-throughput synthesis and specificity characterization of natively paired influenza hemagglutinin antibodies with oPoolScience translational medicine · 2025Article
- Cryo-EM led analysis of open and closed conformations of Chagas vaccine candidate TcPOP.Nature communications · 2025Article
- Slice'N'Dice: maximizing the value of predicted models for structural biologists.Acta crystallographica. Section D, Structural biology · 2025Article
- ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.Protein science : a publication of the Protein Society · 2024Article
- Likelihood-based interactive local docking into cryo-EM maps in ChimeraX.Acta crystallographica. Section D, Structural biology · 2024Article
- Integrative Approaches to Study Virus Structures.Sub-cellular biochemistry · 2024Review
- The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.Acta crystallographica. Section D, Structural biology · 2023Article
- UCSF ChimeraX: Tools for structure building and analysis.Protein science : a publication of the Protein Society · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimized strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.
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Registered trials
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